For me it was near the end where that guy you meet under the sea (can't believe I forgot) walks through the portal to the Ninth Underworld. It was so sweet and sad to see him innocently sing his song and soldier on into portal, never to be seen again. It reminded me of how far Manny has gone and how soon his (and my) journey will end. It's hard to explain but it's the moment that really touched me.

Agree!
I don't know how to explain neither, but for me it was like if the game was finishing in that moment and that was a general goodbye or something like that.